ICI Sex Project

This repository contains code for analyzing sex-based differences in immune checkpoint inhibitor (ICI) response.

Project Structure

project_root/
├── docs/                                   # Documentation
├── output/                                 # Analysis outputs and results
├── pair_clinical_data_and_stages_of_tumors # Pipeline for pairing clinical data and stages of tumors as well as specification, description, dictionary, and testing
├── processed_data/                         # Processed data files
├── src/                                    # Source code
│   ├── cd8_analysis/                       # CD8+ T cell analysis
│   ├── data_processing/                    # Data processing utilities
│   ├── icb_analysis/                       # Immune checkpoint blockade analysis
│   ├── immune_analysis/                    # Immune signature analysis
│   ├── sex_stratified/                     # Sex-stratified analysis
│   └── utils/                              # Shared utility functions
├── requirements.txt                        # Python dependencies
└── setup.sh                                # Environment setup script

Setup

Environment Setup

1. Make the setup script executable and run it:

chmod +x setup.sh
./setup.sh

2. Activate the conda environment:

source miniconda3/etc/profile.d/conda.sh
conda activate ici_sex

Dependencies

Dependencies are installed by setup.sh.

Modules

CD8 Analysis

Analysis of CD8+ T cell signatures in RNA-seq data. See CD8 Analysis README for details.

ICB Analysis

Analysis of immune checkpoint blockade medications and their relationship with CD8+ T cell signatures. See ICB Analysis README for details.

Immune Analysis

Analysis of immune signatures and tumor microenvironment. See Immune Analysis README for details.

Sex-Stratified Analysis

Sex-stratified analysis of immune signatures and treatment response.

Usage

Each module can be run independently. For example:

# Run ICB analysis
python -m src.icb_analysis.icb_main

# Run CD8 group analysis
python src/cd8_analysis/cd8_groups_analysis.py

See individual module READMEs for more details.

Processed Data

The processed data directory contains processed data files used in the analyses. Raw data is not included in this repository.

Results

Analysis results are saved to the output directory, organized by analysis type.